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Old 07-20-2011, 04:45 AM   #1
Graham Etherington
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Default Extract perfectly mapped reads from SAM/BAM file

Hi,
Given a SAM or BAM file, does anyone know how to identify which paired-sequences map perfectly to the reference? By perfectly mapped, I mean that the query is identical to the the reference (or its reverse complement).
I'm fine using either command-line tools or programming.
Many thanks,
Graham
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Old 07-20-2011, 07:44 AM   #2
dariober
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Hi,
I think you can look at the NM tag in the SAM/BAM file. If both reads of a pair have NM:i:0 than the match is perfect.

Dario
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Old 07-21-2011, 07:27 AM   #3
nilshomer
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Make sure that there is also no soft-clipping in the cigar if you want the full read aligned.
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